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Update fragment_types.py to add SanitizeMol calls #61

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Update fragment_types.py to add SanitizeMol calls #61

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4 changes: 4 additions & 0 deletions mmpdblib/fragment_types.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,6 +258,8 @@ def __init__(
self.max_up_enumerations = max_up_enumerations

def normalize(self, mol):
from rdkit import Chem
Chem.SanitizeMol(mol)
# XXX Remove existing isotope labels?
if self.salt_remover is not None:
desalted_mol = self.salt_remover.StripMol(mol)
Expand All @@ -269,6 +271,8 @@ def normalize(self, mol):
return None, desalted_mol

def apply_filters(self, mol):
from rdkit import Chem
Chem.SanitizeMol(mol)
num_heavies = 0
for atom in mol.GetAtoms():
atomic_num = atom.GetAtomicNum()
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